Description

The function constructs an object of class TranscriptionDataSet,
which is a container for holding processed sequencing data and the results of
all downstream analyses. All the slots of the created object are filled
during the workflow by applying specific functions to the object directly.

Numeric. Extend read length to the fragment size.
Default: 250.

unique

paired.end

Logical. Whether to treat a BAM file as paired-end.
Default: FALSE.

swap.strand

Logical. Whether to reverse the strand of the read.
Default: FALSE.

param

ScanBamParam object influencing what
fields and which records (reads) are imported from a BAM file. Default:
NULL.

Details

The slots fragments, fragmentSize, region,
coveragePlus, coverageMinus are filled during the object
construction. The fragments holds information about genomic
coordinates of the sequenced fragments (reads extended to the fragmento
size). coveragePlus and coverageMinus for each position in
the genome counts the number of fragments that cover it (for the details,
see coverage). region holds information about
the region used for fragments extraction.

Value

An object of class TranscriptionDataSet.

Author(s)

Armen R. Karapetyan

Examples

1
2
3
4
5

### Load TranscriptionDataSet objectdata(tds)### View a short summary of the objecttds